I have not tried so I cannot answer definitively but I'd think so. Question is if the software you want to use afterwards understands it. I guess you have two "functions"? You could split those apart with the scanEvent filter. You'd need that filter also to get rid of the lockmass scans.

btw.: I had some MS/MS data today where I used the lockmassRefiner. That seemed to do something wrong. On the other hand it seemed that with my data I got the calibrated data which was not the case with previous versions. So for calibrated data compare with your vendor software to check that the peaks have the right mass.

Yes, my raw data have two "functions":1) "intact compound" m/z ; 2) fragment pattern. Then I'll process them using XCMS R-package.I'll check the Proteowizard's filters and learn more about these filters that you are telling me. I've been using MSconvertGUI to convert my raw data. Thank you so much. I was worry about that.

The problem with using proteowizard is that I am pretty sure waters tags their MSe data as 'MS1' - the logic being their is no precursor selection. Since the data are not tagged as MS2, the proteowizard filters do not work. I use proteowizard whenever i have either MS1 data only, or MS1 data with dedicate MS/MS data. For MSe I still use databridge run from the acquisition sequence table. If you have found a solution within proteowizard for MSe with the goal of bringing it to XCMS, do let me know, as I would be very interested in trying it out as well.

I can't say that I remember how this worked, though I think I did try it. If I recall, the problem is that you have to know which scan events (by integer number) are MS and which are MSE and which are LockMass. I think that if you have that data, or can extract it in an efficient manner, it would work, but I never figured out an efficient way. Not to say it can't be done, I just haven't done it.